ABC Two-Dimensional Variant Classification System — ESHG Guide
The ABC system (Houge et al., European Journal of Human Genetics, 2022; doi: 10.1038/s41431-021-00903-z) classifies variants on two independent axes — Grade A (functional/molecular evidence) and Grade B (clinical/phenotypic evidence) — then combines them in a 2D matrix to produce a final classification class (A to F, or 0).
Grade A — Functional/Molecular Evidence (6 levels)
A0 — fVUS (Functional VUS): No usable functional data. Variant type unknown. Always Class 0.
A1 — NF (Normal Function): Allele frequency >1% in gnomAD, or documented benign polymorphism in ClinVar, or frequent ancestral allele. Always Class 0.
A2 — LNF (Likely Normal Function): Allele frequency 0.1–1%, or synonymous without splicing impact, or low conservation in non-haploinsufficient gene. Always Class 0.
A3 — HFE (Hypothetical Functional Effect): Rare variant with unfavorable in silico predictions only. No direct functional studies. Functionally uncharacterized region.
A4 — LFE (Likely Functional Effect): Truncating in haploinsufficient gene (NMD not confirmed), missense at active site or critical domain, or partial/indirect functional data supporting LOF.
A5 — FE (Proven Functional Effect): Published in vitro or in vivo functional study demonstrating pathogenic effect, NMD confirmed by RT-PCR, or demonstrated loss of enzymatic activity.
Grade B — Clinical/Phenotypic Evidence (6 levels)
B0 — cVUS (Clinical VUS / Discordant Gene): Gene outside patient phenotype, or incidental finding with no known association to clinical presentation. Always Class 0 or F.
B1 — VOI (Variant of Interest): Gene in the right metabolic pathway, or association not formally established, or potential candidate with fewer than 3 published families.
B2 — RF (Risk Factor): Single pathogenic allele in AR gene with compatible phenotype, or dominant variant with low penetrance (<20%). Examples: CFTR heterozygous, APOE ε4.
B3 — Path↑ (Pathogenic, High Penetrance): Confirmed biallelic AR variant (2 alleles), or well-established dominant with penetrance ≥80%. Examples: BRCA2 truncating, TP53 Li-Fraumeni.
B4 — Path↔ (Pathogenic, Moderate Penetrance): Dominant variant with penetrance 20–40%, or unaffected individual in an affected family.
B5 — Path↑↑ (Pathogenic, Very High Penetrance): Penetrance >40% in a very well-established clinical context. Examples: BRCA2 familial breast/ovarian, TP53 confirmed Li-Fraumeni syndrome.
ABC Classification Matrix (Grade A × Grade B)
A0, A1, A2 → always Class 0 regardless of Grade B.
A3 × B0 → F | A3 × B1–B2 → E | A3 × B3–B5 → D
A4 × B0–B1 → E | A4 × B2–B3 → D | A4 × B4 → C | A4 × B5 → B
A5 × B0 → E | A5 × B1 → D | A5 × B2–B3 → D/C | A5 × B4 → B | A5 × B5 → A
Final Classification Classes
Class A: Pathogenic — high penetrance. Must be returned to the patient.
Class B: Pathogenic — moderate penetrance. To be returned to the patient.
Class C: Pathogenic — variant to be returned depending on clinical context.
Class D: Pathogenic candidate — report depending on context and phenotype match.
Class E: Variant of Interest (VOI) — uncertain significance, insufficient evidence for classification.
Class F: Discordant gene — variant unlikely to explain this patient's phenotype.
Class 0: Insufficient functional data (Grade A ≤ 2) or discordant gene (Grade B = 0).